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Shao F, Pan H, Li P, Ni L, Xu Y, Peng Z. Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish ( Hemibagrus wyckioides). Front Genet 2021; 12:747684. [PMID: 34712270 PMCID: PMC8546334 DOI: 10.3389/fgene.2021.747684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/27/2021] [Indexed: 12/21/2022] Open
Affiliation(s)
- Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Huamei Pan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Ping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China.,College of Fisheries, Southwest University, Chongqing, China
| | - Luyun Ni
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Yuan Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, China
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2
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Comparative cytogenomic analysis of Cardinal fishes (Perciformes, Apogonidae) from Thailand. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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3
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Yeesin P, Buasriyot P, Ditcharoen S, Chaiyasan P, Suwannapoom C, Juntaree S, Jantarat S, Talumphai S, Cioffi MDB, Liehr T, Tanomtong A, Supiwong W. Comparative study of four Mystus species (Bagridae, Siluriformes) from Thailand: insights into their karyotypic diversity. COMPARATIVE CYTOGENETICS 2021; 15:119-136. [PMID: 33959235 PMCID: PMC8093182 DOI: 10.3897/compcytogen.v15i2.60649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Karyotypes of four catfishes of the genus Mystus Scopoli, 1777 (family Bagridae), M. atrifasciatus Fowler, 1937, M. mysticetus Roberts, 1992, M. singaringan (Bleeker, 1846) and M. wolffii (Bleeker, 1851), were analysed by conventional and Ag-NOR banding as well as fluorescence in situ hybridization (FISH) techniques. Microsatellite d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeat probes were applied in FISH. The obtained data revealed that the four studied species have different chromosome complements. The diploid chromosome numbers (2n) and the fundamental numbers (NF) range between 52 and 102, 54 and 104, 56 and 98, or 58 and 108 in M. mysticetus, M. atrifasciatus, M. singaringan or M. wolffii, respectively. Karyotype formulae of M. mysticetus, M. atrifasciatus, M. singaringan and M. wolffii are 24m+26sm+4a, 26m+24sm+2a, 24m+18sm+14a and 30m+22sm+6a, respectively. A single pair of NORs was identified adjacent to the telomeres of the short arm of chromosome pairs 3 (metacentric) in M. atrifasciatus, 20 (submetacentric) in M. mysticetus, 15 (submetacentric) in M. singaringan, and 5 (metacentric) in M. wolffii. The d(GC)15, d(CAA)10, d(CAT)10 and d(GAA)10 repeats were abundantly distributed in species-specific patterns. Overall, we present a comparison of cytogenetic and molecular cytogenetic patterns of four species from genus Mystus providing insights into their karyotype diversity in the genus.
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Affiliation(s)
- Pun Yeesin
- Department of Technology and Industries, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Muang, Pattani 94000, Thailand
| | - Phichaya Buasriyot
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Sukhonthip Ditcharoen
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Patcharaporn Chaiyasan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, Thailand
| | - Sippakorn Juntaree
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani Campus, Mueng, Pattani 94000, Thailand
| | - Sucheela Talumphai
- Major Biology, Department of Science and Technology, Faculty of Liberal Arts and Science, Roi Et Rajabhat University, Roi Et 45120, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747, Jena, Germany
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Weerayuth Supiwong
- Applied Science Program, Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen University, Muang, Nong Khai 43000, Thailand
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4
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Ditcharoen S, Sassi FDMC, Bertollo LAC, Molina WF, Liehr T, Saenjundaeng P, Tanomtong A, Supiwong W, Suwannapoom C, Cioffi MDB. Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species. Genet Mol Biol 2020; 43:e20200091. [PMID: 33156890 PMCID: PMC7654372 DOI: 10.1590/1678-4685-gmb-2020-0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/03/2020] [Indexed: 01/08/2023] Open
Abstract
The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
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Affiliation(s)
- Sukhonthip Ditcharoen
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Francisco de Menezes Cavalcante Sassi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Luiz Antonio Carlos Bertollo
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do NorteUniversidade Federal do Rio Grande do NorteDepartamento de Biologia Celular e GenéticaNatalRNBrazilUniversidade Federal do Rio Grande do Norte (UFRN), Centro de
Biociências, Departamento de Biologia Celular e Genética, Natal, RN,
Brazil.
| | - Thomas Liehr
- University Hospital JenaUniversity Hospital JenaInstitute of Human GeneticsJenaGermanyUniversity Hospital Jena, Institute of Human Genetics, Jena,
Germany.
| | - Pasakorn Saenjundaeng
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Alongklod Tanomtong
- Khon Kaen UniversityKhon Kaen UniversityDepartment of BiologyMuangKhon KaenThailandKhon Kaen University, Faculty of Science, Department of
Biology, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen,
Thailand.
| | - Weerayuth Supiwong
- Khon Kaen UniversityKhon Kaen UniversityFaculty of Applied Science and EngineeringMuangNong KhaiThailandKhon Kaen University, Faculty of Applied Science and
Engineering, Nong Khai Campus, Muang, Nong Khai, Thailand.
| | - Chatmongkon Suwannapoom
- University of PhayaoUniversity of PhayaoDepartment of FisherySchool of Agriculture and Natural ResourcesMuang PhayaoThailandUniversity of Phayao, School of Agriculture and Natural
Resources, Department of Fishery, Muang Phayao, Thailand.
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos
(UFSCar)Universidade Federal de São Carlos (UFSCar)Departamento de Genética e
EvoluçãoSão CarlosSPBrazilUniversidade Federal de São Carlos (UFSCar),
Departamento de Genética e Evolução, São Carlos, SP,
Brazil.
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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6
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Karyotype analysis and nucleolar organizer regions (NORs) of Sundaic yellow catfish, Hemibagrus capitulum (Siluriformes, Siluridae) in Thailand. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00321-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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7
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Phimphan S, Aiumsumang S, Tanomtong A, Jantarat S. Karyomorphological delineation and linear differentiation of microsatellite patterns, and meiosis in giant Asian river frog (Limnonectes blyhii) from Thailand. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00315-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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8
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Phimphan S, Chaiyasan P, Suwannapoom C, Reungsing M, Juntaree S, Tanomtong A, Supiwong W. Comparative karyotype study of three Cyprinids (Cyprinidae, Cyprininae) in Thailand by classical cytogenetic and FISH techniques. COMPARATIVE CYTOGENETICS 2020; 14:597-612. [PMID: 33384854 PMCID: PMC7772283 DOI: 10.3897/compcytogen.v14i4.54428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/27/2020] [Indexed: 05/13/2023]
Abstract
Three species of ornamental fishes in the subfamily Cyprininae (family Cyprinidae) namely, Epalzeorhynchos frenatum (Fowler, 1934), Puntigrus partipentazona (Fowler, 1934), Scaphognathops bandanensis Boonyaratpalin et Srirungroj, 1971 were studied by classical cytogenetic and fluorescent in situ hybridization (FISH) techniques. Chromosomes were directly prepared from kidney tissues and stained by using conventional and Ag-NOR banding techniques. Microsatellite d(CA)15 and d(CGG)10 probes were hybridized to the chromosomes of three cyprinids. The results show that the three cyprinid species share the same diploid number as 2n=50 but there are differences in the fundamental number (NF) and karyotypes i.e. E. frenatum: NF = 78, 18m+10sm+10st+12a; P. partipentazona: NF = 80, 6m+24sm+14st+6a; S. bandanensis: NF = 66, 4m+12sm+34a. NOR positive masks were observed at the regions adjacent to the telomere of the short arm of the chromosome pairs 10 (submetacentric) and 1 (metacentric) in E. frenatum and P. partipentazona, respectively whereas those were revealed at telomeric regions of the long arm of the chromosome pair 9 (acrocentric) in S. bandanensis. The mapping of d(CA)15 and d(CGG)10 microsatellites shown that hybridization signals are abundantly distributed in telomeric regions of several pairs except d(CA)15 repeats in S. bandanensis, which are distributed throughout all chromosomes and d(CGG)10 repeats in P. partipentazona display the high accumulation only in the first chromosome pair.
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Affiliation(s)
- Sumalee Phimphan
- Biology program, Faculty of Science and Technology, Phetchabun Rajabhat University, Phetchabun 67000, ThailandPhetchabun Rajabhat UniversityPhetchabunThailand
| | - Patcharaporn Chaiyasan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao 56000, ThailandUniversity of PhayaoPhayaoThailand
| | - Montri Reungsing
- Department of Biotechnology, Faculty of Science and Technology, Rajamangala University of Technology Tawan-ok, Sri Racha, Chon Buri 20110, ThailandRajamangala UniversityChon BuriThailand
| | - Sippakorn Juntaree
- Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen, University, Muang, Nong Khai 43000, ThailandKhon Kaen UniversityNong KhaiThailand
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Nong Khai Campus, Khon Kaen, University, Muang, Nong Khai 43000, ThailandKhon Kaen UniversityNong KhaiThailand
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Liu Y, Song M, Luo W, Xia Y, Zeng X. Chromosomal Evolution in the Amolops mantzorum Species Group (Ranidae; Anura) Narrated by Repetitive DNAs. Cytogenet Genome Res 2019; 157:172-178. [PMID: 30955010 DOI: 10.1159/000499416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
In an attempt to analyze the organization of repetitive DNAs in the amphibian genome, 7 microsatellite motifs and a 5S rDNA sequence were synthesized and mapped in the karyotypes of 5 Amolops species. The results revealed nonrandom distribution of the microsatellite repeats, usually in the heterochromatic regions, as found in other organisms. These microsatellite repeats showed rapid changes among Amolops species, documenting the recent evolutionary history within this lineage. In contrast, 5S rDNA was localized in chromosomes 5 of all species, suggesting that these chromosomes are homologous within the monophyletic clade. Furthermore, the heteromorphic X and Y sex chromosomes (chromosomes 5) of A.mantzorum, had identical patterns of 5S rDNA, indicating that the subtelocentric Y resulted from a pericentric inversion. Several microsatellite repeats were found in the heteromorphic sex chromosomes, verifying the association of repetitive DNAs with sex chromosome differentiation in A. mantzorum.
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Supiwong W, Pinthong K, Seetapan K, Saenjundaeng P, Bertollo LAC, de Oliveira EA, Yano CF, Liehr T, Phimphan S, Tanomtong A, B Cioffi M. Karyotype diversity and evolutionary trends in the Asian swamp eel Monopterus albus (Synbranchiformes, Synbranchidae): a case of chromosomal speciation? BMC Evol Biol 2019; 19:73. [PMID: 30849933 PMCID: PMC6408769 DOI: 10.1186/s12862-019-1393-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Synbranchidae or swamp eels are fishes belonging to the order Synbranchiformes that occur in both freshwater and occasionally in brackish. They are worldwide distributed in tropical and subtropical rivers of four different continents. A large degree of chromosomal variation has been found in this family, mainly through the use of conventional cytogenetic investigations. Inside this group, a still almost unexplored species under the cytogenetic point of view is the Asian swamp eel Monopterus albus, a widely distributed species throughout Asia. Here, we tested the hypothesis of chromosomal speciation, where a case of sympatric speciation may occur as the primary consequence of chromosomal rearrangements. We performed a comparative chromosomal analysis of M. albus from 22 different localities in Thailand, using distinct staining methods (C-banding, Ag-NO3, and Chromomycin A3), and FISH with repetitive DNA probes (5S rDNA, 18S rDNA, Rex1 element and microsatellite repeats). RESULTS This approach evidenced two contrasting karyotypes (named karyomorphs A and B) that varied concerning their 2n and repetitive DNAs distribution, where chromosomal fusions and pericentric inversions were involved in such differentiation. While the karyomorph A has 2n = 24 chromosomes, the karyomorph B has only 2n = 18, both with NF = 24. In addition, karyomorph A contains only acrocentric chromosomes, while karyomorph B contains three unique metacentric pairs. These features highlight that M. albus has already gone through a significant genomic divergence, and may include at least two cryptic species. CONCLUSIONS This marked chromosomal differentiation, likely linked to the lifestyle of these fishes, point to the occurrence of a chromosomal speciation scenario, in which fusions and inversions had a prominent role. This highlights the biodiversity of M. albus and justifies its taxonomic revision, since this nominal species may constitute a species complex.
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Affiliation(s)
- Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Surin, 32000 Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao, 56000 Thailand
| | - Pasakorn Saenjundaeng
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, 34000 Thailand
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Sumalee Phimphan
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen, 40002 Thailand
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
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11
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Carducci F, Barucca M, Canapa A, Biscotti MA. Rex Retroelements and Teleost Genomes: An Overview. Int J Mol Sci 2018; 19:ijms19113653. [PMID: 30463278 PMCID: PMC6274825 DOI: 10.3390/ijms19113653] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 01/29/2023] Open
Abstract
Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
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Utsunomia R, Melo S, Scacchetti PC, Oliveira C, Machado MDA, Pieczarka JC, Nagamachi CY, Foresti F. Particular Chromosomal Distribution of Microsatellites in Five Species of the Genus Gymnotus (Teleostei, Gymnotiformes). Zebrafish 2018; 15:398-403. [PMID: 29927722 DOI: 10.1089/zeb.2018.1570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microsatellites show great abundance in eukaryotic genomes, although distinct chromosomal distribution patterns might be observed, from small dispersed signals to strong clustered motifs. In Neotropical fishes, the chromosome mapping of distinct microsatellites was employed several times to uncover the origin and evolution of sex and supernumerary chromosomes, whereas a detailed comparative analysis considering different motifs at the chromosomal level is scarce. Here, we report the chromosomal location of several simple sequence repeats (SSRs) in distinct electric knife fishes showing variable diploid chromosome numbers to unveil the structural organization of several microsatellite motifs in distinct Gymnotus species. Our results showed that some SSRs are scattered throughout the genomes, whereas others are particularly clustered displaying intense genomic compartmentalization. Interestingly, the motifs CA, GA, and GAG exhibited a band-like pattern of hybridization, useful for the identification of homologous chromosomes. Finally, the colocalization of SSRs with multigene families is probably related to the association of microsatellites with gene spacers in this case.
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Affiliation(s)
- Ricardo Utsunomia
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Silvana Melo
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Priscilla Cardim Scacchetti
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Claudio Oliveira
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
| | - Milla de Andrade Machado
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Julio Cesar Pieczarka
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Cleusa Yoshiko Nagamachi
- 2 Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará , Belém, PA, Brazil
| | - Fausto Foresti
- 1 Laboratório de Biologia e Genética de Peixes, Department of Morphology, Institute of Biosciences of Botucatu, São Paulo State University , Botucatu, SP, Brazil
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Supiwong W, Jiwyam W, Sreeputhorn K, Maneechot N, Bertollo LAC, Cioffi MB, Getlekha N, Tanomtong A. First report on classical and molecular cytogenetics of archerfish, Toxotes chatareus (Perciformes: Toxotidae). THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0216-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Costa GWWF, Cioffi MDB, Bertollo LAC, Molina WF. Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum). Zebrafish 2015; 12:215-20. [PMID: 25719607 DOI: 10.1089/zeb.2014.1077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.
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Affiliation(s)
- Gideão W W F Costa
- 1 Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte , Natal, Brazil
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